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Starlitnightly / omicverse

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
https://starlitnightly.github.io/omicverse/
GNU General Public License v3.0
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the error cNMF #107

Closed zhoushican closed 2 weeks ago

zhoushican commented 1 month ago 
cnmf_obj.consensus(k=selected_K, 
                   density_threshold=density_threshold, 
                   show_clustering=True, 
                   close_clustergram_fig=False)

error

{
    "name": "TypeError",
    "message": "H should have the same dtype as X. Got H.dtype = float32.",
    "stack": "---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[26], line 1
----> 1 cnmf_obj.consensus(k=selected_K, 
      2                    density_threshold=density_threshold, 
      3                    show_clustering=True, 
      4                    close_clustergram_fig=False)

File ~/mambaforge/envs/omicverse_gpu/lib/python3.10/site-packages/omicverse/single/_cnmf.py:838, in cNMF.consensus(self, k, density_threshold, local_neighborhood_size, show_clustering, skip_density_and_return_after_stats, close_clustergram_fig, refit_usage)
    835     spectra_tpm_rf = spectra_tpm.loc[:,hvgs]
    837     spectra_tpm_rf = spectra_tpm_rf.div(tpm_stats.loc[hvgs, '__std'], axis=1)
--> 838     rf_usages = self.refit_usage(norm_tpm.X, spectra_tpm_rf)
    839     rf_usages = pd.DataFrame(rf_usages, index=norm_counts.obs.index, columns=spectra_tpm_rf.index)                                                                  
    841 save_df_to_npz(median_spectra, self.paths['consensus_spectra']%(k, density_threshold_repl))

File ~/mambaforge/envs/omicverse_gpu/lib/python3.10/site-packages/omicverse/single/_cnmf.py:667, in cNMF.refit_usage(self, X, spectra)
    664 else:
    665     refit_nmf_kwargs.update(dict(n_components = spectra.shape[0], H = spectra, update_H = False))
--> 667 _, rf_usages = self._nmf(X, nmf_kwargs=refit_nmf_kwargs)
    668 if (type(X) is pd.DataFrame) and (type(spectra) is pd.DataFrame):
    669     rf_usages = pd.DataFrame(rf_usages, index=X.index, columns=spectra.index)

File ~/mambaforge/envs/omicverse_gpu/lib/python3.10/site-packages/omicverse/single/_cnmf.py:546, in cNMF._nmf(self, X, nmf_kwargs)
    535 def _nmf(self, X, nmf_kwargs):
    536     \"\"\"
    537     Parameters
    538     ----------
   (...)
    544 
    545     \"\"\"
--> 546     (usages, spectra, niter) = non_negative_factorization(X, **nmf_kwargs)
    548     return(spectra, usages)

File ~/mambaforge/envs/omicverse_gpu/lib/python3.10/site-packages/sklearn/utils/_param_validation.py:214, in validate_params.<locals>.decorator.<locals>.wrapper(*args, **kwargs)
    208 try:
    209     with config_context(
    210         skip_parameter_validation=(
    211             prefer_skip_nested_validation or global_skip_validation
    212         )
    213     ):
--> 214         return func(*args, **kwargs)
    215 except InvalidParameterError as e:
    216     # When the function is just a wrapper around an estimator, we allow
    217     # the function to delegate validation to the estimator, but we replace
    218     # the name of the estimator by the name of the function in the error
    219     # message to avoid confusion.
    220     msg = re.sub(
    221         r\"parameter of \\w+ must be\",
    222         f\"parameter of {func.__qualname__} must be\",
    223         str(e),
    224     )

File ~/mambaforge/envs/omicverse_gpu/lib/python3.10/site-packages/sklearn/decomposition/_nmf.py:1122, in non_negative_factorization(X, W, H, n_components, init, update_H, solver, beta_loss, tol, max_iter, alpha_W, alpha_H, l1_ratio, random_state, verbose, shuffle)
   1119 X = check_array(X, accept_sparse=(\"csr\", \"csc\"), dtype=[np.float64, np.float32])
   1121 with config_context(assume_finite=True):
-> 1122     W, H, n_iter = est._fit_transform(X, W=W, H=H, update_H=update_H)
   1124 return W, H, n_iter

File ~/mambaforge/envs/omicverse_gpu/lib/python3.10/site-packages/sklearn/decomposition/_nmf.py:1670, in NMF._fit_transform(self, X, y, W, H, update_H)
   1663     raise ValueError(
   1664         \"When beta_loss <= 0 and X contains zeros, \"
   1665         \"the solver may diverge. Please add small values \"
   1666         \"to X, or use a positive beta_loss.\"
   1667     )
   1669 # initialize or check W and H
-> 1670 W, H = self._check_w_h(X, W, H, update_H)
   1672 # scale the regularization terms
   1673 l1_reg_W, l1_reg_H, l2_reg_W, l2_reg_H = self._compute_regularization(X)

File ~/mambaforge/envs/omicverse_gpu/lib/python3.10/site-packages/sklearn/decomposition/_nmf.py:1202, in _BaseNMF._check_w_h(self, X, W, H, update_H)
   1200 _check_init(H, (self._n_components, n_features), \"NMF (input H)\")
   1201 if H.dtype != X.dtype:
-> 1202     raise TypeError(
   1203         \"H should have the same dtype as X. Got H.dtype = {}.\".format(
   1204             H.dtype
   1205         )
   1206     )
   1207 # 'mu' solver should not be initialized by zeros
   1208 if self.solver == \"mu\":

TypeError: H should have the same dtype as X. Got H.dtype = float32."
}

https://omicverse.readthedocs.io/en/latest/Tutorials-single/t_cnmf/ https://github.com/dylkot/cNMF/issues/10

Starlitnightly commented 1 month ago

@DBinary Please resolve this issue.

zhoushican commented 1 month ago

The demo data from this tutorial is used. [(https://omicverse.readthedocs.io/en/latest/Tutorials-single/t_cnmf/)]

packages in environment at omicverse_gpu:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_kmp_llvm conda-forge absl-py 2.1.0 pyhd8ed1ab_0 conda-forge adjusttext 1.2.0 pyhd8ed1ab_0 conda-forge aiohttp 3.9.5 py310h2372a71_0 conda-forge aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge alembic 1.13.2 pypi_0 pypi anndata 0.10.8 pyhd8ed1ab_0 conda-forge annotated-types 0.7.0 pyhd8ed1ab_0 conda-forge annoy 1.17.3 pypi_0 pypi anyio 4.4.0 pyhd8ed1ab_0 conda-forge aom 3.9.1 hac33072_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py310h2372a71_4 conda-forge arpack 3.9.1 nompi_h77f6705_101 conda-forge array-api-compat 1.7.1 pyhd8ed1ab_0 conda-forge arrow 1.3.0 pyhd8ed1ab_0 conda-forge ase 3.23.0 pyhd8ed1ab_0 conda-forge astor 0.8.1 pyh9f0ad1d_0 conda-forge asttokens 2.4.1 pyhd8ed1ab_0 conda-forge async-lru 2.0.4 pyhd8ed1ab_0 conda-forge async-timeout 4.0.3 pyhd8ed1ab_0 conda-forge atk-1.0 2.38.0 hd4edc92_1 conda-forge attrs 23.2.0 pyh71513ae_0 conda-forge autograd 1.6.2 pyhd8ed1ab_0 conda-forge autograd-gamma 0.5.0 pyh9f0ad1d_0 conda-forge autopage 0.5.2 pypi_0 pypi aws-c-auth 0.7.20 h5f1c8d9_0 conda-forge aws-c-cal 0.6.12 h2ba76a8_0 conda-forge aws-c-common 0.9.17 h4ab18f5_0 conda-forge aws-c-compression 0.2.18 h36a0aea_4 conda-forge aws-c-event-stream 0.4.2 h161de36_10 conda-forge aws-c-http 0.8.1 h63f54a0_13 conda-forge aws-c-io 0.14.8 h96d4d28_0 conda-forge aws-c-mqtt 0.10.4 hcc7299c_2 conda-forge aws-c-s3 0.5.9 h10bd90f_0 conda-forge aws-c-sdkutils 0.1.16 h36a0aea_0 conda-forge aws-checksums 0.1.18 h36a0aea_4 conda-forge aws-crt-cpp 0.26.8 h4f3a3cc_11 conda-forge aws-sdk-cpp 1.11.267 h51dfee4_8 conda-forge babel 2.14.0 pyhd8ed1ab_0 conda-forge backoff 2.2.1 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.12.3 pyha770c72_0 conda-forge biopython 1.84 pypi_0 pypi bioservices 1.11.2 pypi_0 pypi bleach 6.1.0 pyhd8ed1ab_0 conda-forge blessed 1.19.1 pyhe4f9e05_2 conda-forge blinker 1.8.2 pyhd8ed1ab_0 conda-forge blosc 1.21.5 hc2324a3_1 conda-forge bokeh 3.4.2 pyhd8ed1ab_0 conda-forge boltons 24.0.0 pyhd8ed1ab_0 conda-forge boto3 1.34.144 pyhd8ed1ab_0 conda-forge botocore 1.34.144 pyge310_1234567_0 conda-forge branca 0.7.2 pyhd8ed1ab_0 conda-forge brotli 1.1.0 hd590300_1 conda-forge brotli-bin 1.1.0 hd590300_1 conda-forge brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge bzip2 1.0.8 h4bc722e_7 conda-forge c-ares 1.32.2 h4bc722e_0 conda-forge ca-certificates 2024.7.4 hbcca054_0 conda-forge cachecontrol 0.14.0 pyhd8ed1ab_1 conda-forge cachecontrol-with-filecache 0.14.0 pyhd8ed1ab_1 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 5.4.0 pyhd8ed1ab_0 conda-forge cairo 1.18.0 h3faef2a_0 conda-forge captum 0.6.0 pyhd8ed1ab_0 conda-forge cattrs 23.2.3 pypi_0 pypi certifi 2024.7.4 pyhd8ed1ab_0 conda-forge cffi 1.16.0 py310h2fee648_0 conda-forge cfitsio 4.3.1 hbdc6101_0 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge chex 0.1.86 pypi_0 pypi cleo 2.1.0 pyhd8ed1ab_0 conda-forge click 8.1.7 unix_pyh707e725_0 conda-forge cliff 4.7.0 pypi_0 pypi cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge cmaes 0.10.0 pypi_0 pypi cmake 3.30.0 pypi_0 pypi cmd2 2.4.3 pypi_0 pypi colorama 0.4.6 pyhd8ed1ab_0 conda-forge colorcet 3.1.0 pyhd8ed1ab_0 conda-forge colorlog 6.8.2 pypi_0 pypi comm 0.2.2 pyhd8ed1ab_0 conda-forge contextlib2 21.6.0 pyhd8ed1ab_0 conda-forge contourpy 1.2.1 py310hd41b1e2_0 conda-forge crashtest 0.4.1 pyhd8ed1ab_0 conda-forge croniter 1.4.1 pyhd8ed1ab_0 conda-forge cryptography 42.0.8 py310hb1bd9d3_0 conda-forge ctxcore 0.2.0 pypi_0 pypi cubinlinker 0.3.0 py310hfdf336d_1 rapidsai cucim 24.02.00 cuda11_py310_240212_g7d08ffc_0 rapidsai cuda-cudart 11.8.89 0 nvidia cuda-cupti 11.8.87 0 nvidia cuda-libraries 11.8.0 0 nvidia cuda-nvrtc 11.8.89 0 nvidia cuda-nvtx 11.8.86 0 nvidia cuda-profiler-api 11.8.86 0 nvidia cuda-python 11.8.3 py310hf9913ef_0 nvidia cuda-runtime 11.8.0 0 nvidia cuda-version 11.8 h70ddcb2_3 conda-forge cudatoolkit 11.8.0 h4ba93d1_13 conda-forge cudf 24.02.02 cuda11_py310_240227_gdd34fdbe35_0 rapidsai cudf_kafka 24.02.02 cuda11_py310_240227_gdd34fdbe35_0 rapidsai cudnn 8.9.7.29 hbc23b4c_3 conda-forge cugraph 24.02.00 cuda11_py310_240213_g3e5f47d0f_0 rapidsai cuml 24.02.00 cuda11_py310_240213_geb50e481d_0 rapidsai cuproj 24.02.00 cuda11_py310_240213_ga881c4a5_0 rapidsai cupy 13.2.0 py310h189a05f_0 conda-forge cupy-core 13.2.0 py310h71e26cc_0 conda-forge cusparselt 0.5.0.1 hd5ab71f_1 conda-forge cuspatial 24.02.00 cuda11_py310_240213_ga881c4a5_0 rapidsai custreamz 24.02.02 cuda11_py310_240227_gdd34fdbe35_0 rapidsai cutensor 2.0.1.2 hcdd5f01_0 conda-forge cuxfilter 24.02.00 cuda11_py310_240213_g4a431d7_0 rapidsai cycler 0.12.1 pyhd8ed1ab_0 conda-forge cyrus-sasl 2.1.27 h54b06d7_7 conda-forge cython 3.0.10 pypi_0 pypi cytoolz 0.12.3 py310h2372a71_0 conda-forge dask 2024.1.1 pyhd8ed1ab_0 conda-forge dask-core 2024.1.1 pyhd8ed1ab_0 conda-forge dask-cuda 24.02.00 py310_240212_g96bedbc_0 rapidsai dask-cudf 24.02.02 cuda11_py310_240227_gdd34fdbe35_0 rapidsai datashader 0.16.3 pyhd8ed1ab_0 conda-forge datetime 5.5 pypi_0 pypi dateutils 0.6.12 py_0 conda-forge dav1d 1.2.1 hd590300_0 conda-forge dbus 1.13.6 h5008d03_3 conda-forge debugpy 1.8.2 py310h76e45a6_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge deepdiff 7.0.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge deprecated 1.2.14 pypi_0 pypi dill 0.3.8 pyhd8ed1ab_0 conda-forge distlib 0.3.8 pyhd8ed1ab_0 conda-forge distributed 2024.1.1 pyhd8ed1ab_0 conda-forge dlpack 0.5 h9c3ff4c_0 conda-forge dm-tree 0.1.8 py310ha8c1f0e_4 conda-forge dnspython 2.6.1 pyhd8ed1ab_1 conda-forge docrep 0.3.2 pyh44b312d_0 conda-forge dulwich 0.21.7 py310h2372a71_0 conda-forge easydev 0.13.2 pypi_0 pypi einops 0.8.0 pyhd8ed1ab_0 conda-forge email-validator 2.2.0 pyhd8ed1ab_0 conda-forge email_validator 2.2.0 hd8ed1ab_0 conda-forge entrypoints 0.4 pyhd8ed1ab_0 conda-forge et_xmlfile 1.1.0 pyhd8ed1ab_0 conda-forge etils 1.7.0 pyhd8ed1ab_0 conda-forge exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge executing 2.0.1 pyhd8ed1ab_0 conda-forge expat 2.6.2 h59595ed_0 conda-forge fa2 0.3.5 py310h5764c6d_2 conda-forge fastapi 0.111.1 pyhd8ed1ab_0 conda-forge fastapi-cli 0.0.4 pyhd8ed1ab_0 conda-forge fastrlock 0.8.2 py310hc6cd4ac_2 conda-forge fbpca 1.0 pypi_0 pypi filelock 3.15.4 pyhd8ed1ab_0 conda-forge flask 3.0.3 pyhd8ed1ab_0 conda-forge flax 0.8.5 pyhd8ed1ab_0 conda-forge fmt 10.2.1 h00ab1b0_0 conda-forge folium 0.17.0 pyhd8ed1ab_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 h77eed37_2 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.53.1 py310h5b4e0ec_0 conda-forge formulaic 1.0.2 pyhd8ed1ab_0 conda-forge fqdn 1.5.1 pyhd8ed1ab_0 conda-forge freetype 2.12.1 h267a509_2 conda-forge freexl 2.0.0 h743c826_0 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge frozendict 2.4.4 pypi_0 pypi frozenlist 1.4.1 py310h2372a71_0 conda-forge fsspec 2024.6.1 pyhff2d567_0 conda-forge future 1.0.0 pyhd8ed1ab_0 conda-forge gdal 3.8.1 py310haaa150b_3 conda-forge gdk-pixbuf 2.42.10 h829c605_5 conda-forge gdown 5.2.0 pyhd8ed1ab_0 conda-forge geopandas 1.0.1 pyhd8ed1ab_0 conda-forge geopandas-base 1.0.1 pyha770c72_0 conda-forge geos 3.12.1 h59595ed_0 conda-forge geosketch 1.2 pypi_0 pypi geotiff 1.7.1 hf074850_14 conda-forge get-annotations 0.1.2 pyhd8ed1ab_0 conda-forge gettext 0.22.5 h59595ed_2 conda-forge gettext-tools 0.22.5 h59595ed_2 conda-forge gevent 24.2.1 pypi_0 pypi gflags 2.2.2 he1b5a44_1004 conda-forge giflib 5.2.2 hd590300_0 conda-forge glog 0.7.1 hbabe93e_0 conda-forge glpk 5.0 h445213a_0 conda-forge gmock 1.14.0 ha770c72_2 conda-forge gmp 6.3.0 hac33072_2 conda-forge gmpy2 2.1.5 py310hc7909c9_1 conda-forge graphite2 1.3.13 h59595ed_1003 conda-forge graphlib-backport 1.0.3 pyhd8ed1ab_0 conda-forge graphtools 1.5.3 pypi_0 pypi graphviz 9.0.0 h78e8752_1 conda-forge greenlet 3.0.3 pypi_0 pypi grequests 0.7.0 pypi_0 pypi grpcio 1.62.2 py310h1b8f574_0 conda-forge gseapy 0.10.8 pypi_0 pypi gtest 1.14.0 h434a139_2 conda-forge gtk2 2.24.33 h280cfa0_4 conda-forge gts 0.7.6 h977cf35_4 conda-forge h11 0.14.0 pyhd8ed1ab_0 conda-forge h2 4.1.0 pyhd8ed1ab_0 conda-forge h5py 3.11.0 nompi_py310hf054cd7_102 conda-forge harfbuzz 8.3.0 h3d44ed6_0 conda-forge harmonypy 0.0.10 pypi_0 pypi hdf4 4.2.15 h2a13503_7 conda-forge hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge hnswlib 0.7.0 py310hcb52e73_2 conda-forge holoviews 1.19.1 pyhd8ed1ab_0 conda-forge hpack 4.0.0 pyh9f0ad1d_0 conda-forge httpcore 1.0.5 pyhd8ed1ab_0 conda-forge httpx 0.27.0 pyhd8ed1ab_0 conda-forge hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge icu 73.2 h59595ed_0 conda-forge idna 3.7 pyhd8ed1ab_0 conda-forge igraph 0.10.13 hef0740d_0 conda-forge imagecodecs-lite 2019.12.3 py310h261611a_8 conda-forge imageio 2.34.2 pyh12aca89_0 conda-forge importlib-metadata 8.0.0 pyha770c72_0 conda-forge importlib_metadata 8.0.0 hd8ed1ab_0 conda-forge importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge inflect 7.3.1 pypi_0 pypi inquirer 3.1.4 pyhd8ed1ab_0 conda-forge interface_meta 1.3.0 pyhd8ed1ab_0 conda-forge intervaltree 3.1.0 pypi_0 pypi ipykernel 6.29.5 pyh3099207_0 conda-forge ipython 8.26.0 pyh707e725_0 conda-forge ipywidgets 8.1.3 pyhd8ed1ab_0 conda-forge isodate 0.6.1 pyhd8ed1ab_0 conda-forge isoduration 20.11.0 pyhd8ed1ab_0 conda-forge itsdangerous 2.2.0 pyhd8ed1ab_0 conda-forge jaraco.classes 3.4.0 pyhd8ed1ab_1 conda-forge jax 0.4.27 pyhd8ed1ab_0 conda-forge jaxlib 0.4.23 cuda118py310hd0f2884_202 conda-forge jaxopt 0.8.3 pyhd8ed1ab_0 conda-forge jbig 2.1 h7f98852_2003 conda-forge jedi 0.19.1 pyhd8ed1ab_0 conda-forge jeepney 0.8.0 pyhd8ed1ab_0 conda-forge jinja2 3.1.4 pyhd8ed1ab_0 conda-forge jmespath 1.0.1 pyhd8ed1ab_0 conda-forge joblib 1.4.2 pyhd8ed1ab_0 conda-forge json-c 0.17 h1220068_1 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zhoushican commented 1 month ago

I tried many times, but the error still exists.

Starlitnightly commented 2 weeks ago

We have fixed this error in omicverse 1.6.6